I am trying to trim adapaters and there is a thing that doesn't quite make sense to me. I've done some simplifications in the description here to focus on the issue. Thanks in advance for any help on the matter.
I've had two samples sequenced with Illumina HiSeq 2000, 50 PE in the same line.
Sample 1 has indexes (barcodes)
Sample 2 has indexes
Note that both samples have same index 2.
When I try to trim for the adapters in mate 1 of sample 1, I sometimes find indexes from sample 2. See example below.
As far as I am concerned, this should not happen.
I've tried to read up on the theories on how this work as good as I can, but cannot find a good explanation for this phenomena. Is there a rational explanation to this? What am I missing?
Thanks,
I've had two samples sequenced with Illumina HiSeq 2000, 50 PE in the same line.
Sample 1 has indexes (barcodes)
Code:
TAAGGCGA and [COLOR="Blue"]TAGATCGC[/COLOR]
Code:
[B][COLOR="DarkGreen"]GCTACGCT[/COLOR][/B] and [COLOR="blue"]TAGATCGC[/COLOR]
When I try to trim for the adapters in mate 1 of sample 1, I sometimes find indexes from sample 2. See example below.
Code:
[B]Sample 1, mate 1[/B] @HISEQ2:697:H2NFYBCXX:1:1101:11477:57300 1:N:0:TAAGGCGA[COLOR="Blue"]TAGATCGC[/COLOR] [COLOR="DarkOrange"]TCTCCGAGCCCACGAGAC[/COLOR][B][COLOR="DarkGreen"]GCTACGCT[/COLOR][/B][COLOR="Red"]ATCTCGTATGCCGTCTTCTGCTTG[/COLOR]A + D@DDBCEHHIIIIHIIIIIIIIIHIDHE?HHHIEEGHHHEHCHFEFG@CHH
As far as I am concerned, this should not happen.
I've tried to read up on the theories on how this work as good as I can, but cannot find a good explanation for this phenomena. Is there a rational explanation to this? What am I missing?
Thanks,
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